Processing a taxatable post MBC and illumina_post_MBC_script2.R
read and print settings
## settings:
## ## bastoolsDir : chr "/home/tutorial/TOOLS/bastools/"
## email : chr "basegeter@gmail.com"
## filter_dxn : num 20
## filter_dxn2 : num 0
## neg.groups : chr [1:2] "Sample_Plate" "extraction_batch"
## neg.types : chr [1:2] "PCR_negative" "Extraction_Negative"
## plotting.vars : chr [1:2] "biomaterial" "bleach_step"
## problemTaxa : chr "NothingToAdd"
## real : chr "swab"
## remove.entire.dataset : logi TRUE
## rep.rm : chr "biomaterial"
## rep.rm.first : logi FALSE
## rep.rm.second : logi FALSE
## rm.only.less.than : logi TRUE
## samplepc : num 0.5
## subsetlist : List of 5
## $ experiment_id : chr "HSJUN19BAS"
## $ primer_set : chr "trnL"
## $ MPLX : chr "N"
## $ substudy : chr "swabtest"
## $ Replicate_Name: chr "ZYMO"
## sumrepsby : chr "biomaterial"
## taxa.to.group : NULL
## taxatabs : chr "/media/sf_Documents/WORK/G-DRIVE/G-WORK/SHARED_FOLDERS/CRAYFISH/rebin/CRAY-HSJUN19BAS_trnl.none.flash2.vsearch_"| __truncated__
## taxonpc : num 0
## unwantedTaxa : chr "NothingToAdd"
## url : chr "https://docs.google.com/spreadsheets/d/1KZLoXHTgtkD0btSWjyAmFiGJ_cPcYITyfFSlzehisRI/edit#gid=1531090624"
## use.contamination.filter : logi TRUE
## xLevel : chr "family"##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionorganise mastersheet
## Reading from 'CRAYFISH_FINAL_datasheet'## Range "'Master_Samplesheet'"## New names:
## * index -> index...6
## * index -> index...8## Removing duplicated columns## Checks only include the mostly used headers, please check to see all desired headers exist## Subsetting datasheet## $experiment_id
## [1] "HSJUN19BAS"
##
## $primer_set
## [1] "trnL"
##
## $MPLX
## [1] "N"
##
## $substudy
## [1] "swabtest"
##
## $Replicate_Name
## [1] "ZYMO"## , , MPLX = N, substudy = swabtest, Replicate_Name = ZYMO
##
## primer_set
## experiment_id trnL
## HSJUN19BAS 44import taxatabs
## Loading required package: tidyverse## ── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──## ✓ tibble 2.1.3 ✓ purrr 0.3.3
## ✓ tidyr 1.0.2 ✓ stringr 1.4.0
## ✓ readr 1.3.1 ✓ forcats 0.4.0## ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()## /media/sf_Documents/WORK/G-DRIVE/G-WORK/SHARED_FOLDERS/CRAYFISH/rebin/CRAY-HSJUN19BAS_trnl.none.flash2.vsearch_qfilt.cutadapt.vsearch_uniq.vsearch_afilt.allsamples_step5.ALL_vsearch_uniq.nodenoise.noclust.rebins.taxatable.tf.spliced.ALTEREDNAMES.txt## reads: 14590984, taxa: 784, samples: 729## Read counts all good## merged taxatable## reads: 14590984, taxa: 784, samples: 729remove problem taxa - usually human, predator, NAs and no_hits
## Removing no_hits## Removing NAs - sequences that had blast hits but were not assigned to any taxon## Removing problem taxa## Checking negs## Ignoring the following taxa: NA;NA;NA;NA;NA;NA;NA & no_hits;no_hits;no_hits;no_hits;no_hits;no_hits;no_hits## from 2 Extraction_Negative samples 2 contained reads## taxon
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;Crithmum;Crithmum maritimum
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;Cymopterus;Cymopterus sessiliflorus
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;Meum;Meum athamanticum
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fabales;Fabaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;Castanea;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;Castanopsis;Castanopsis carlesii
## Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Danthoniopsis;Danthoniopsis dinteri
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Dinebra;NA
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Festuca;Festuca kolymensis
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Muhlenbergia;NA
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Paspalum;Paspalum dilatatum
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Paspalum;Paspalum notatum
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Paspalum;Paspalum thunbergii
## Eukaryota;Streptophyta;Magnoliopsida;Ranunculales;Ranunculaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;unknown;NA;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;Cissus;NA
## Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS CRAY-ECsZY-ZYMO-2-trnL-HSBAS
## 5 0
## 2 0
## 4 0
## 1181 0
## 0 287
## 139 0
## 9 0
## 2 0
## 778 0
## 9 0
## 2 0
## 3 0
## 13 0
## 1118 0
## 2 0
## 7 0
## 9 0
## 18 0
## 4475 0
## 0 12
## 0 843## from 2 PCR_negative samples 1 contained reads## taxon
## Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;Brassica;Brassica oleracea
## Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;Brassica;Brassica souliei
## Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Rosales;Rosaceae;Rubus;Rubus idaeus
## Eukaryota;Streptophyta;Pinopsida;Pinales;Pinaceae;Picea;NA
## Eukaryota;Streptophyta;Pinopsida;Pinales;Pinaceae;Picea;Picea neoveitchii
## Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;Athyrium;NA
## Eukaryota;Streptophyta;unknown;unknown;NA;NA;NA
## CRAY-34NC2-ZYMO-2-trnL-HSBAS
## 2
## 2
## 796
## 2
## 12
## 8
## 486
## 2333## Making quantile plots to help deciding dxn_filter threshold## Using taxon as id variables
## Using taxon as id variables
## Making barplots for only those taxa detected in both negatives and real samples - to help decide taxon filter and rm.contaminants filter
## Using taxon as id variables
## Making barplots for only those taxa detected in both negatives and real samples - to help decide sample filter
## Using taxon as id variables
## Using taxon as id variables
apply taxon and sample filters
## Applying taxon_pc filter.## Using filter of 0 %. reads removed: 0 from 247738 ; detections removed: 0 from 471## Applying sample_pc filter. Note: this removes samples with no reads## Using filter of 0.5 %. reads removed: 1647 from 247738 ; detections removed: 286 from 471## Checking negs## Ignoring the following taxa: NA;NA;NA;NA;NA;NA;NA & no_hits;no_hits;no_hits;no_hits;no_hits;no_hits;no_hits## from 2 Extraction_Negative samples 2 contained reads## taxon
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fabales;Fabaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;unknown;NA;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;Cissus;NA
## Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS CRAY-ECsZY-ZYMO-2-trnL-HSBAS
## 1181 0
## 0 287
## 139 0
## 778 0
## 1118 0
## 4475 0
## 0 12
## 0 843## from 2 PCR_negative samples 1 contained reads## taxon
## Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA
## Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;Athyrium;NA
## Eukaryota;Streptophyta;unknown;unknown;NA;NA;NA
## CRAY-34NC2-ZYMO-2-trnL-HSBAS
## 796
## 486
## 2333## Making quantile plots to help deciding dxn_filter threshold## Using taxon as id variables
## Using taxon as id variables
## Making barplots for only those taxa detected in both negatives and real samples - to help decide taxon filter and rm.contaminants filter
## Using taxon as id variables
## Making barplots for only those taxa detected in both negatives and real samples - to help decide sample filter
## Using taxon as id variables
## Using taxon as id variables
remove detection in less than 2 reps (only done here if rep.rm.first is TRUE)
PCR negatives are exempt, if the negative option is set (only makes sense pre-rm.contaminants function, or without rm.contaminants function)
apply detection filter
## Applying detection filter## Using detection filter of 20 : reads removed: 65 from 246091 ; detections removed: 5 from 185## Checking negs## Ignoring the following taxa: NA;NA;NA;NA;NA;NA;NA & no_hits;no_hits;no_hits;no_hits;no_hits;no_hits;no_hits## from 2 Extraction_Negative samples 2 contained reads## taxon
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fabales;Fabaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;unknown;NA;NA;NA
## Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS CRAY-ECsZY-ZYMO-2-trnL-HSBAS
## 1181 0
## 0 287
## 139 0
## 778 0
## 1118 0
## 4475 0
## 0 843## from 2 PCR_negative samples 1 contained reads## taxon
## Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA
## Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;Athyrium;NA
## Eukaryota;Streptophyta;unknown;unknown;NA;NA;NA
## CRAY-34NC2-ZYMO-2-trnL-HSBAS
## 796
## 486
## 2333## Making quantile plots to help deciding dxn_filter threshold## Using taxon as id variables
## Using taxon as id variables
## Making barplots for only those taxa detected in both negatives and real samples - to help decide taxon filter and rm.contaminants filter
## Using taxon as id variables
## Making barplots for only those taxa detected in both negatives and real samples - to help decide sample filter
## Using taxon as id variables
## Using taxon as id variables
remove contaminants from relevant groups
## Applying contaminant filter## Only removing detections which had a read count less than the negtive## Based on Extraction_Negative CRAY-ECsZY-ZYMO-1-trnL-HSBAS , Removing detections of## [1] "Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA"
## [2] "Eukaryota;Streptophyta;Magnoliopsida;Fabales;Fabaceae;NA;NA"
## [3] "Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;NA;NA"
## [4] "Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;NA;NA"
## [5] "Eukaryota;Streptophyta;Magnoliopsida;unknown;NA;NA;NA"## if it occurred in any samples belonging to extraction_batch:batchSWB_ZY## 34479 reads removed from 21 detection(s) in 26 sample(s), of which 7691 were in the negative. See table below for details:## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS 1181
## CRAY-SWB1_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-2-trnL-HSBAS 3767
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 1563
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P21-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P21-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P4-ZYMO-1-trnL-HSBAS 4011
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-1-trnL-HSBAS 4863
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 1280
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 762
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 1407
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P2-ZYMO-1-trnL-HSBAS 4391
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 1756
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 847
## CRAY-SWB2_P8-ZYMO-1-trnL-HSBAS 705
## Eukaryota;Streptophyta;Magnoliopsida;Fabales;Fabaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS 139
## CRAY-SWB1_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 262
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 541
## CRAY-SWB1_P21-ZYMO-1-trnL-HSBAS 2868
## CRAY-SWB1_P21-ZYMO-2-trnL-HSBAS 835
## CRAY-SWB1_P4-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 685
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P2-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P8-ZYMO-1-trnL-HSBAS 0
## Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS 778
## CRAY-SWB1_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P21-ZYMO-1-trnL-HSBAS 1053
## CRAY-SWB1_P21-ZYMO-2-trnL-HSBAS 236
## CRAY-SWB1_P4-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P2-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P8-ZYMO-1-trnL-HSBAS 0
## Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS 1118
## CRAY-SWB1_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-1-trnL-HSBAS 1435
## CRAY-SWB1_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 410
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 1991
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P21-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P21-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P4-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 1799
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 542
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P2-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 311
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 2881
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P8-ZYMO-1-trnL-HSBAS 217
## Eukaryota;Streptophyta;Magnoliopsida;unknown;NA;NA;NA
## CRAY-ECsZY-ZYMO-1-trnL-HSBAS 4475
## CRAY-SWB1_P10-ZYMO-2-trnL-HSBAS 1289
## CRAY-SWB1_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P12-ZYMO-2-trnL-HSBAS 3155
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 1869
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 2942
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 943
## CRAY-SWB1_P21-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P21-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P4-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 1490
## CRAY-SWB1_P8-ZYMO-1-trnL-HSBAS 2494
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 1353
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 2227
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 2088
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 1171
## CRAY-SWB2_P2-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 1005
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 2632
## CRAY-SWB2_P8-ZYMO-1-trnL-HSBAS 0## Based on Extraction_Negative CRAY-ECsZY-ZYMO-2-trnL-HSBAS , Removing detections of## [1] "Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA"
## [2] "Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA"## if it occurred in any samples belonging to extraction_batch:batchSWB_ZY## 5674 reads removed from 11 detection(s) in 21 sample(s), of which 1130 were in the negative. See table below for details:## Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA
## CRAY-ECsZY-ZYMO-2-trnL-HSBAS 287
## CRAY-SWB1_P14-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P16-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 639
## CRAY-SWB2_P21-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P21-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 0
## CRAY-SWB2_P8-ZYMO-2-trnL-HSBAS 0
## Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA
## CRAY-ECsZY-ZYMO-2-trnL-HSBAS 843
## CRAY-SWB1_P14-ZYMO-1-trnL-HSBAS 884
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 449
## CRAY-SWB1_P16-ZYMO-2-trnL-HSBAS 1512
## CRAY-SWB1_P19-ZYMO-1-trnL-HSBAS 1448
## CRAY-SWB1_P19-ZYMO-2-trnL-HSBAS 796
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 214
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 609
## CRAY-SWB1_P8-ZYMO-2-trnL-HSBAS 1017
## CRAY-SWB2_P10-ZYMO-1-trnL-HSBAS 295
## CRAY-SWB2_P10-ZYMO-2-trnL-HSBAS 485
## CRAY-SWB2_P12-ZYMO-1-trnL-HSBAS 805
## CRAY-SWB2_P12-ZYMO-2-trnL-HSBAS 1004
## CRAY-SWB2_P16-ZYMO-2-trnL-HSBAS 1414
## CRAY-SWB2_P19-ZYMO-1-trnL-HSBAS 1638
## CRAY-SWB2_P19-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P21-ZYMO-1-trnL-HSBAS 322
## CRAY-SWB2_P21-ZYMO-2-trnL-HSBAS 302
## CRAY-SWB2_P4-ZYMO-2-trnL-HSBAS 261
## CRAY-SWB2_P6-ZYMO-1-trnL-HSBAS 1586
## CRAY-SWB2_P8-ZYMO-2-trnL-HSBAS 806## Based on PCR_negative CRAY-34NC2-ZYMO-2-trnL-HSBAS , Removing detections of## [1] "Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA"
## [2] "Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;Athyrium;NA"
## [3] "Eukaryota;Streptophyta;unknown;unknown;NA;NA;NA"## if it occurred in any samples belonging to Sample_Plate:34## 11425 reads removed from 6 detection(s) in 6 sample(s), of which 3615 were in the negative. See table below for details:## Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA
## CRAY-34NC2-ZYMO-2-trnL-HSBAS 796
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 82
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P21-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 1564
## Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;Athyrium;NA
## CRAY-34NC2-ZYMO-2-trnL-HSBAS 486
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 1669
## CRAY-SWB2_P21-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 0
## Eukaryota;Streptophyta;unknown;unknown;NA;NA;NA
## CRAY-34NC2-ZYMO-2-trnL-HSBAS 2333
## CRAY-SWB1_P14-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB1_P2-ZYMO-2-trnL-HSBAS 127
## CRAY-SWB1_P6-ZYMO-2-trnL-HSBAS 0
## CRAY-SWB2_P21-ZYMO-2-trnL-HSBAS 59
## CRAY-SWB2_P6-ZYMO-2-trnL-HSBAS 0## ***********A total of 51578 reads removed## ****Furthermore, removing the following contaminant taxa from entire dataset## [1] "Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA"
## [2] "Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;Athyrium;NA"
## [3] "Eukaryota;Streptophyta;unknown;unknown;NA;NA;NA"
## [4] "Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA"
## [5] "Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA"## ***********A further 976 reads removed## Checking that all negatives are now clean## Ignoring the following taxa: NA;NA;NA;NA;NA;NA;NA & no_hits;no_hits;no_hits;no_hits;no_hits;no_hits;no_hits## No negatives found with readsremove detection in less than 2 reps
PCR negatives are exempt, if the negative option is set (only makes sense pre-rm.contaminants function, or without rm.contaminants function)
sum reps
## If only one rep, will keep that repapply 2nd detection filter (possibly makes more sense here?)
## Applying detection filter## Using detection filter of 0 : reads removed: 0 from 193472 ; detections removed: 0 from 127aggregate at chosen level and keep only that-level taxa
## Reminder: this changes 'unknown' and 'collapsed' to 'NA'## Removing NAs and no_hitsremove unwanted taxa for analysis
## Removing unwanted taxasummary —this is pre-grouping - please inspect, add groupings to config file as necessary and look at post-grouping table. Can more grouping be done, is anything wrong?
## Skipping grouping of taxagroup taxa, where possible
if(is.null(taxa.to.group)){
message("Skipping grouping of taxa")
} else {
for(i in 1:nrow(taxa.to.group)){
all.taxatabs.ss<-bas.group.taxa(taxatab = all.taxatabs.ss,taxon=as.character(taxa.to.group[i,1]), jointo=as.character(taxa.to.group[i,2]))
}
stepcounter<-stepcounter+1
all.stats[[stepcounter]]<-taxatab.sumStats(all.taxatabs.ss,stepname = "group_taxa")
}## Skipping grouping of taxasummary–post-grouping
## Skipping grouping of taxasome barplots
## Making barplots## If column names are not ss_sample_ids using 'grouping' to specify what they are## Using taxon as id variables## Outputting as a list where first element is plot and second is legend
## If column names are not ss_sample_ids using 'grouping' to specify what they are## Using taxon as id variables## Outputting as a list where first element is plot and second is legend
## If column names are not ss_sample_ids using 'grouping' to specify what they are## Using taxon as id variables## Outputting as a list where first element is plot and second is legend
## If column names are not ss_sample_ids using 'grouping' to specify what they are## Using taxon as id variables## Outputting as a list where first element is plot and second is legend
## If column names are not ss_sample_ids using 'grouping' to specify what they are## Using taxon as id variables## Outputting as a list where first element is plot and second is legend
## If column names are not ss_sample_ids using 'grouping' to specify what they are## Using taxon as id variables## Outputting as a list where first element is plot and second is legend
pca plot (just an example, not interesting in this case)
## Plotting pca plot with lines## Assuming grouping has already been done## Principal Component Analysis plot of community simmilarity using Bray-Curtis distances## Note: Ellipses will not be calculated if there are groups with too few data points## ellipses are drawn with a confidence level of 0.90## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse## Assuming grouping has already been done## Principal Component Analysis plot of community simmilarity using Bray-Curtis distances## Note: Ellipses will not be calculated if there are groups with too few data points## ellipses are drawn with a confidence level of 0.90
## Plotting pca plot without lines## Assuming grouping has already been done## Principal Component Analysis plot of community simmilarity using Bray-Curtis distances## Note: Ellipses will not be calculated if there are groups with too few data points## ellipses are drawn with a confidence level of 0.90## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse## Assuming grouping has already been done## Principal Component Analysis plot of community simmilarity using Bray-Curtis distances## Note: Ellipses will not be calculated if there are groups with too few data points## ellipses are drawn with a confidence level of 0.90
combine counts and taxalists
## Note that detections/samples after sumreps will be fewer because reps are joined## detections reads taxa samples step
## 1 481 264378 208 41 start
## 2 473 247750 207 41 rm.nohits
## 3 471 247738 206 41 rm.non-assigned
## 4 471 247738 206 41 rm.problem
## 5 471 247738 206 41 taxonpc
## 6 185 246091 52 41 samplepc
## 7 180 246026 51 40 dxnfilter
## 8 140 193472 50 37 rm.contaminants
## 9 127 193472 50 19 sumreps
## 10 127 193472 50 19 dxnfilter2
## 11 114 193472 34 19 aggregate_by_xLevel
## 12 111 189664 31 19 keep_only_xLevel
## 13 111 189664 31 19 unwanted## The taxalist output needs more work, depends on collapsed taxa, need to split nto 2 tables, pre and post collapse.
## Running pre-aggregate_by_xLevel only. Some clever way to plot this?final taxa list
## [1] Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA
## [2] Eukaryota;Streptophyta;Magnoliopsida;Apiales;Araliaceae;NA;NA
## [3] Eukaryota;Streptophyta;Magnoliopsida;Asparagales;Amaryllidaceae;NA;NA
## [4] Eukaryota;Streptophyta;Magnoliopsida;Asterales;Asteraceae;NA;NA
## [5] Eukaryota;Streptophyta;Magnoliopsida;Brassicales;Brassicaceae;NA;NA
## [6] Eukaryota;Streptophyta;Magnoliopsida;Ericales;Actinidiaceae;NA;NA
## [7] Eukaryota;Streptophyta;Magnoliopsida;Ericales;Primulaceae;NA;NA
## [8] Eukaryota;Streptophyta;Magnoliopsida;Fabales;Fabaceae;NA;NA
## [9] Eukaryota;Streptophyta;Magnoliopsida;Fagales;Betulaceae;NA;NA
## [10] Eukaryota;Streptophyta;Magnoliopsida;Fagales;Fagaceae;NA;NA
## [11] Eukaryota;Streptophyta;Magnoliopsida;Fagales;Juglandaceae;NA;NA
## [12] Eukaryota;Streptophyta;Magnoliopsida;Gentianales;Rubiaceae;NA;NA
## [13] Eukaryota;Streptophyta;Magnoliopsida;Lamiales;Plantaginaceae;NA;NA
## [14] Eukaryota;Streptophyta;Magnoliopsida;Laurales;Lauraceae;NA;NA
## [15] Eukaryota;Streptophyta;Magnoliopsida;Malpighiales;Euphorbiaceae;NA;NA
## [16] Eukaryota;Streptophyta;Magnoliopsida;Malpighiales;Salicaceae;NA;NA
## [17] Eukaryota;Streptophyta;Magnoliopsida;Malvales;Malvaceae;NA;NA
## [18] Eukaryota;Streptophyta;Magnoliopsida;Myrtales;Lythraceae;NA;NA
## [19] Eukaryota;Streptophyta;Magnoliopsida;Poales;Cyperaceae;NA;NA
## [20] Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;NA;NA
## [21] Eukaryota;Streptophyta;Magnoliopsida;Rosales;Moraceae;NA;NA
## [22] Eukaryota;Streptophyta;Magnoliopsida;Rosales;Rhamnaceae;NA;NA
## [23] Eukaryota;Streptophyta;Magnoliopsida;Rosales;Rosaceae;NA;NA
## [24] Eukaryota;Streptophyta;Magnoliopsida;Sapindales;Rutaceae;NA;NA
## [25] Eukaryota;Streptophyta;Magnoliopsida;Sapindales;Simaroubaceae;NA;NA
## [26] Eukaryota;Streptophyta;Magnoliopsida;Solanales;Solanaceae;NA;NA
## [27] Eukaryota;Streptophyta;Magnoliopsida;Vitales;Vitaceae;NA;NA
## [28] Eukaryota;Streptophyta;Magnoliopsida;Zingiberales;Musaceae;NA;NA
## [29] Eukaryota;Streptophyta;Pinopsida;Pinales;Pinaceae;NA;NA
## [30] Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Athyriaceae;NA;NA
## [31] Eukaryota;Streptophyta;Polypodiopsida;Polypodiales;Dennstaedtiaceae;NA;NA
## 31 Levels: Eukaryota;Streptophyta;Magnoliopsida;Apiales;Apiaceae;NA;NA ...plot counts
## Note that detections/samples after sumreps will be fewer because reps are joined
